Systems Biology Graduate and Undergraduate Educational Programs

Systems biology graduate students are recruited to SDCSB laboratories through two distinct programs, both of which our faculty helped initiate: the new qBio specialization and the established Bioinformatics and Systems Biology (BISB) program. Relevant to the curricula of these programs, SDCSB faculty members routinely develop and maintain teaching modules on quantitative modeling, clustering and classification, genetic screens, network mapping and other systems biology techniques. BISB also offers a matching degree program for undergraduates. SDCSB investigators are frequent sponsors of undergraduate research in their laboratories, in many cases using SDCSB funding and resources.

UCSD iGEM Teams

In 2014, the SDCSB sponsored a team of 9 UCSD undergraduates for the international genetically engineered machines (iGEM) competition, an international competition for undergraduate and high school students that focuses on synthetic biology. The team developed a Cytoscape-based web tool called SBiDer for engineering genetic circuits. In 2015, the SDCSB sponsored a team of 6 UCSD undergraduates who are trying to develop rapid approaches for identifying rate-limiting steps in metabolic pathways. More information about these teams and projects can be found here.

Demonstration Projects in Systems Biomedicine

In 2015, the SDCSB along with the UCSD Center for Computational Biology & Bioinformatics (CCBB) issued an request for applications (RFA) for “Demonstration Projects in Systems Biomedicine.” This RFA sought to fund projects within UCSD Health Sciences trying to develop and apply systems biology datasets and approaches to address a compelling biomedical question. We received over 30 applications and funded 3 projects. More details about this program and the winning projects can be found here.

Organization of International and Regional Meetings

A key aspect of the SDCSB educational mission is to organize meetings that provide a global and/or regional stage for systems biology research and education.  Our signature international conference is the Winter q-bio Meeting in Hawaii (also 2016, 2015, 2014 and 2013), first organized by SDCSB faculty members Jeff Hasty, Alex Hoffmann and Lev Tsimring in 2013 with funding from SDCSB.

Starting in 2015, we initiated two new regional events. In collaboration with the NIAID-funded FluOMICS and FluDyNeMo Programs, we organized the Systems Analysis of Host-Pathogen Interactions Symposium, which featured national and local thought leaders discussing current gaps in our understanding of how pathogens evade host immune surveillance to establish acute and chronic infections.

With help from Mohit Jain, an Assistant Professor of Pharmacology and Medicine at UCSD, the SDCSB organized a Metabolomics Conference. This event featured nationally and internationally renowned scientists discussing their work in technical mass spectrometry, analytical chemistry and the biological applications of these emerging tools.

In 2015, we started a new Quarterly Systems-to-Synthesis Meeting (also 2015 Fall, 2015 Spring) featuring short talks by graduate students and postdoctoral fellows from labs throughout the SDCSB. In past years, we organized an annual Systems-to-Synthesis Symposium featuring speakers from the local systems biology community and keynote talks from renowned national or international speakers (2014 and 2013).

We also sponsor a regional Southern California Systems Biology Conference in partnership with the Center for Complex Biological Systems, a National Center for Systems Biology at UC Irvine (Arthur Lander, PI).

Organization of Workshops and Tutorials.

The SDCSB has a strong track record of disseminating scientific and technical products to our local community through the organization of workshops and tutorials. A number of the workshops have been developed and are run by staff from the SDCSB Cores in order to educate the community on systems biology experimental and bioinformatic techniques. For example, our annual workshops on Cytoscape and Network Analysis (also 2013 and 2012) and Mathematical Modeling (also 2015, 2014 and 2013) emphasize practical skills for research design and execution and provide guidance for applicable software In previous years, we have also organized workshops focused on the analysis of next-generation sequencing data (2013 and 2012).

The SDCSB is also a sponsor of the q-bio Summer School (also 2014, 2013 and 2012). The q-bio Summer School is an annual event intended to advance predictive modeling of cellular regulatory systems by exposing participants to a survey of work in quantitative biology and by providing in-depth instruction in selected techniques. The summer school is designed for graduate students, postdoctoral fellows or anyone with a quantitative background who is new to modeling cellular regulatory systems.

We continue to organize an annual workshop on Intellectual Property and Licensing (also 2015, 2013 and 2012). This year’s workshop focused on the challenges of patent reform, pertinent recent Supreme Court cases, dealing with patent trolls and the impact of patent reform on technology commercialization.

As part of our partnership with FluOMICS, we also helped to organize a workshop focused on Quantitative Proteomics Approaches to Study Host-Pathogen Relationships. Speakers focused on the latest and most effective methods for probing protein-protein interactions and post-translational modifications as well as practical and computational advice for performing quantitative proteomic studies.

Our computational workshops have recently been consolidated under a new local program called the San Diego Bioinformatics Users Series (SDBUS). SDBUS consists of a monthly meeting in which one or two presenters discuss new software tools and technology in bioinformatics analysis.

We also continue to provide support to local hackathons such as the 1st BD2K 3rd Network of BioThings Hackathon and the 2nd Network of BioThings Hackathon. The most recent event brought together experts in their respective fields to work collectively on solving challenges related to biomedical big data.

Organization of Seminars and Journal Clubs

The SDCSB supports two seminar series at UCSD: the Genetics, Bioinformatics and Systems Biology Colloquium (also 2015-16, 2010 – 2015) and the qBio Seminar Series (also 2016-17, 2015-16, previously the BCI / SDCSB Seminar Series). Both of these well-attended seminar series feature a mix of local and national speakers

In 2014, the SDCSB organized a weekly journal club called “The Greatest Hits of Systems Biology.” The papers discussed included well-cited classics (Milo et al., Science 2002, and Sachs et al., Science 2005) along with more eclectic choices (Savageau et al., PNAS 2009, and Soubannier et al., Curr. Biol. 2012). Presenters included faculty, post-docs, and graduate students from many of the SDCSB-funded labs.

In 2013, the SDCSB hosted weekly breakfast meetings at UC San Diego where we welcomed any persons interested in Systems Biology to participate. The meetings were well received and had attendees from UCSD, GNF, Salk, SBP and TSRI. These meeting were a useful for networking, sharing ideas and creating of collaborations.